Evaluate TF activity: repressions between TFs and targets

Here, we use the code to evaluate methods based on the dyngen simulation, but enforce a more discriminative prior between true and noisy edges.

Generate datasets

library(tidyverse)
library(dyngen)

nIter <- 6
for(nn in 1:nIter){
  # generate a dataset
  set.seed(nn*10)
  backbone <- backbone_linear()
  model <- initialise_model(
    backbone = backbone,
    num_tfs = 100,
    num_targets = 500,
    num_hks = 100,
    tf_network_params = tf_network_default(sample_num_regulators = function() 2),
    feature_network_params = feature_network_default(max_in_degree=20),
    download_cache_dir = "~/.cache/dyngen",
    num_cores = 4,
    simulation_params = simulation_default(
      census_interval = 1,
      compute_cellwise_grn = TRUE
    )
  )
  dataset <- model %>%
    generate_tf_network() %>%
    generate_feature_network() %>%
    generate_kinetics() %>%
    generate_gold_standard() %>%
    generate_cells() %>%
    generate_experiment()
  
  saveRDS(list(model,dataset),
          file = paste0("datasets/simIters/dataset",nn,".rds"))
}

One dataset

library(msigdbr)
library(GSEABase)

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library(viper)
library(AUCell)
library(tidyverse)

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library(dyngen)
ksource <- function(x, ...) {
  library(knitr)
  source(purl(x, output = tempfile()), ...)
}
# install.packages("/domino/edv/chbv-bm-single-cell/KVande/24/transfactorPaper/transfactor/", repos = NULL)
library(transfactor)

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source('../simulateFromModel/20201120_evaluateSimulatedDataset.R')

data <- readRDS("./datasets/simIters/dataset1.rds")
model <- data[[1]]
dataset <- data[[2]]

## plot
### Trajectory
#  doesnt work: install.packages("/domino/edv/chbv-bm-single-cell/KVande/24/transfactorPaper/dynplot/", repos = NULL)
# devtools::install_github(repo="dynverse/dynfeature")
# devtools::install_github(repo="dynverse/dynplot")
library(dynplot)
wrappedDataset <- wrap_dataset(dataset)
# plots an MDS
# g1 <- dynplot::plot_dimred(wrappedDataset,
#             label_milestones = TRUE,
#             size_cells = 1,
#             size_trajectory = 2)

### GRN
g2 <- plot_backbone_modulenet(dataset) + labs(title = "Backbone module reg. net.")
g3 <- plot_feature_network(dataset, show_targets = FALSE) +
            labs(title = "TF reg. net.")
g4 <- plot_feature_network(dataset) + labs(title = "TF + target reg. net.")

g <- patchwork::wrap_plots(g2, g3, g4, byrow = TRUE, ncol = 2, nrow = 2, 
                           widths = rep(1, 2), heights = rep(1, 2)) +
  patchwork::plot_annotation(tag_levels = "A")
# ggsave("../plots/simDataDyngen1Plots.pdf", g, width = 30, height = 15)



countsAll <- t(as.matrix(dataset$experiment$counts_premrna + dataset$experiment$counts_mrna))

# only look at TFs
feature_info <- dataset$feature_info
tf_info <- feature_info %>% filter(is_tf)
feature_network <- dataset$feature_network %>% mutate(name = paste0(from, "->", to))

### get true GRN
tf <- as.character(unique(feature_network$from))
targets <- as.character(unique(feature_network$to))

## full GRN including repressions
XAll <- matrix(0, nrow=length(targets), ncol=length(tf),
            dimnames=list(targets, tf))
for(tt in 1:ncol(XAll)){
  curTF <- tf[tt]
  curTFTargets <- as.character(feature_network[feature_network$from == curTF, "to"][[1]])
  curTFEffects <- feature_network[feature_network$from == curTF, "effect"][[1]]
  XAll[cbind(curTFTargets,curTF)] <- curTFEffects
}
#sort(colSums(abs(XAll))) ; sort(table(feature_network$from)[colnames(XAll)]) #should be same
XAll <- XAll[rowSums(abs(XAll))>0,]
XAll <- XAll[,colSums(abs(XAll))>0]
# remove TFs with only repressions
tfsWithOnlyRepression <- apply(XAll, 2, function(x){
  all(x == 0 | x == -1)
})
XAll <- XAll[,!tfsWithOnlyRepression]
barplot(table(rowSums(abs(XAll))))

barplot(table(colSums(abs(XAll))))

## alpha
alpha <- abs(XAll)
id <- as.matrix(cbind(dataset$feature_network[,2], dataset$feature_network[,1]))
keepId <- id[,1] %in% rownames(XAll) & id[,2] %in% colnames(XAll) & dataset$feature_network$effect == 1
id <- id[keepId,]
# alpha[id] <- dataset$feature_network$strength[keepId]
### more discriminative prior by making this much larger
alpha[id] <- dataset$feature_network$strength[keepId] * 100

# truth: only TFs from burn-in or modules.
truth <- data.frame(de=rep(1, ncol(XAll)),
                    row.names=colnames(XAll))
truth[grep(x=rownames(truth), pattern="Target|HK"),] <- 0


countsTfTargets <- countsAll[rownames(XAll),]

nNoiseEdges <- 500
nNoiseTFs <- 10
XNoisy <- addNoiseToGRN(X = XAll,
                       nNoiseTFs = nNoiseTFs,
                       nNoiseEdges = nNoiseEdges,
                       noiseProb = 3/nrow(XAll),
                       seed = 10)

# truth
truthNoisy <- rbind(truth, data.frame(de=rep(0, nNoiseTFs),
                                      row.names=paste0("noisyTF",1:nNoiseTFs)))

## filter if necessary
keepGene <- rowSums(abs(XNoisy)) > 0
counts <- countsTfTargets[keepGene,]
curAlpha <- alpha[keepGene,]
XNoisy <- XNoisy[keepGene,]
keepTF <- colSums(abs(XNoisy)) > 0
truthNoisy <- truthNoisy[keepTF,,drop=FALSE]

# get true alpha for noisy GRN
if(nNoiseTFs > 0){
  alphaTrueNoisy <- cbind(curAlpha, XNoisy[,(ncol(XAll)+1):(ncol(XAll)+nNoiseTFs)])
} else {
  alphaTrueNoisy <- curAlpha
}
XNoisy <- XNoisy[,keepTF]
alphaTrueNoisy <- alphaTrueNoisy[,keepTF]
alphaTrueNoisy[XNoisy == 0] <- 0
rownames(truthNoisy) <- colnames(XNoisy)
# viper regulon
regulonNoisy <- constructViperRegulon(XNoisy, alphaTrueNoisy)
# AUCell genesets
genesetsNoisy <- constructGenesets(XNoisy, alphaTrueNoisy)

qSteps <- 0.05
pt <- dataset$experiment$cell_info$sim_time
ptGroups <- Hmisc::cut2(pt, cuts = quantile(pt, prob=seq(0,1,by=qSteps)))
Xpt <- model.matrix(~0+ptGroups)
design <- Xpt

res <- evaluateSimulation_repressions(counts = countsAll,
                               design = design,
                               X = XNoisy,
                              alpha = alphaTrueNoisy,
                              regulon = regulonNoisy,
                              genesets = genesetsNoisy,
                              truth = truthNoisy,
                              verbose = TRUE,
                              alphaScale = 1)

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## 
## Attaching package: 'glmGamPoi'

## The following object is masked from 'package:dplyr':
## 
##     vars

## The following object is masked from 'package:ggplot2':
## 
##     vars

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

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## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

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## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

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## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## iteration 1

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 462 links to zero.

## Prior versus data weight is tuned to be 100%.

## iteration 1

## iteration 2. Log-lik: -1081575.363

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## iteration 62. Log-lik: -1051475.914

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## iteration 1

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## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

res$pAll

res$dfAUC

##          auc                      method
## 1  0.6495911                     poisson
## 2  0.7539683                     dirMult
## 3  0.6563252            dirMult_alphaEst
## 4  0.6503127               poisson_lasso
## 5  0.7539683               dirMult_lasso
## 6  0.6565657      dirMult_lasso_alphaEst
## 7  0.6616162          poisson_lasso_repr
## 8  0.7484367          dirMult_lasso_repr
## 9  0.6563252 dirMult_lasso_alphaEst_repr
## 10 0.6772487                       viper
## 11 0.6955267                      AUCell

Over iterations

nNoiseTFGrid <- c(0, ncol(XAll), ncol(XAll)*2, ncol(XAll)*4) # 100% to 33.3% data-generating TFs
nNoiseEdgeGrid <- c(-sum(abs(XAll))/2, -sum(abs(XAll))/4, 0, sum(abs(XAll))*2, sum(abs(XAll))*4) # -50% to +200% true links
nIter <- 6



pNoLeg <- list()
for(nn in 1:nIter){
  # load a dataset
  data <- readRDS(paste0("datasets/simIters/dataset",nn,".rds"))
  model <- data[[1]]
  dataset <- data[[2]]
  
  for(nnTF in 1:length(nNoiseTFGrid)){
    nNoiseTFs <- nNoiseTFGrid[nnTF]
    for(nnEdge in 1:length(nNoiseEdgeGrid)){
      set.seed(nn*10*nnTF*nnEdge)
      nNoiseEdges <- nNoiseEdgeGrid[nnEdge]
      countsAll <- t(as.matrix(dataset$experiment$counts_premrna + dataset$experiment$counts_mrna))
      
      # only look at TFs
      feature_info <- dataset$feature_info
      tf_info <- feature_info %>% filter(is_tf)
      feature_network <- dataset$feature_network %>% mutate(name = paste0(from, "->", to))
      
      ### get true GRN
      tf <- as.character(unique(feature_network$from))
      targets <- as.character(unique(feature_network$to))
      
      ## full GRN including repressions
      XAll <- matrix(0, nrow=length(targets), ncol=length(tf),
                  dimnames=list(targets, tf))
      for(tt in 1:ncol(XAll)){
        curTF <- tf[tt]
        curTFTargets <- as.character(feature_network[feature_network$from == curTF, "to"][[1]])
        curTFEffects <- feature_network[feature_network$from == curTF, "effect"][[1]]
        XAll[cbind(curTFTargets,curTF)] <- curTFEffects
      }
      XAll <- XAll[rowSums(abs(XAll))>0,]
      XAll <- XAll[,colSums(abs(XAll))>0]
      # remove TFs with only repressions
      tfsWithOnlyRepression <- apply(XAll, 2, function(x){
        all(x == 0 | x == -1)
      })
      XAll <- XAll[,!tfsWithOnlyRepression]
      #barplot(table(rowSums(abs(XAll))))
      #barplot(table(colSums(abs(XAll))))
      
      ## alpha
      alpha <- abs(XAll)
      id <- as.matrix(cbind(dataset$feature_network[,2], dataset$feature_network[,1]))
      keepId <- id[,1] %in% rownames(XAll) & id[,2] %in% colnames(XAll) & dataset$feature_network$effect == 1
      id <- id[keepId,]
      # alpha[id] <- dataset$feature_network$strength[keepId]
      ### more discriminative prior by making this much larger
      alpha[id] <- dataset$feature_network$strength[keepId] * 100
      
      
      # truth: only TFs from burn-in or modules.
      truth <- data.frame(de=rep(1, ncol(XAll)),
                          row.names=colnames(XAll))
      truth[grep(x=rownames(truth), pattern="Target|HK"),] <- 0
      
      
      countsTfTargets <- countsAll[rownames(XAll),]
      
      XNoisy <- addNoiseToGRN(X = XAll,
                             nNoiseTFs = nNoiseTFs,
                             nNoiseEdges = nNoiseEdges,
                             noiseProb = 3/nrow(XAll))
      
      # truth
      truthNoisy <- rbind(truth, data.frame(de=rep(0, nNoiseTFs)))
      ## filter if necessary
      keepGene <- rowSums(abs(XNoisy)) > 0
      counts <- countsTfTargets[keepGene,]
      curAlpha <- alpha[keepGene,]
      XNoisy <- XNoisy[keepGene,]
      keepTF <- colSums(abs(XNoisy)) > 0
      truthNoisy <- truthNoisy[keepTF,,drop=FALSE]
      
      # get true alpha for noisy GRN
      if(nNoiseTFs > 0){
        alphaTrueNoisy <- cbind(curAlpha, XNoisy[,(ncol(XAll)+1):(ncol(XAll)+nNoiseTFs)])
      } else {
        alphaTrueNoisy <- curAlpha
      }
      XNoisy <- XNoisy[,keepTF]
      alphaTrueNoisy <- alphaTrueNoisy[,keepTF]
      alphaTrueNoisy[XNoisy == 0] <- 0
      rownames(truthNoisy) <- colnames(XNoisy)
      # viper regulon
      regulonNoisy <- constructViperRegulon(XNoisy, alphaTrueNoisy)
      # AUCell genesets
      genesetsNoisy <- constructGenesets(XNoisy, alphaTrueNoisy)
      
      qSteps <- 0.05
      ptGroups <- Hmisc::cut2(pt, cuts = quantile(dataset$experiment$cell_info$sim_time, prob=seq(0,1,by=qSteps)))
      Xpt <- model.matrix(~0+ptGroups)
      design <- Xpt
          
      
      res <- evaluateSimulation_repressions(counts = countsAll,
                                     design = design,
                                     X = XNoisy,
                                    alpha = alphaTrueNoisy,
                                    regulon = regulonNoisy,
                                    genesets = genesetsNoisy,
                                    truth = truthNoisy,
                                    verbose = FALSE,
                                    alphaScale = 1,
                                    iterMax = 1000)
      
      curDfAUC <- res$dfAUC
      curDfAUC$noiseEdges <- nNoiseEdges
      curDfAUC$noiseTFs <- nNoiseTFs
      curDfAUC$nn <- nn
      
      if(!exists("dfAUCAll")){
        dfAUCAll <- curDfAUC
      } else {
        dfAUCAll <- rbind(dfAUCAll, curDfAUC)
      }
      
    }
  }
  
  saveRDS(dfAUCAll, file=paste0("../objects/dfAUCAll_dyngen",nn,"_discriminativePrior.rds"))
}

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 156 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 156 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 192 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 156 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 83 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 83 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 323 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 83 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 37 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 37 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 393 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 37 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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|======================================================================| 100%

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 88 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 88 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 318 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 88 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 41 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 41 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 411 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 41 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 22 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 22 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 437 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 22 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 35 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 35 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 424 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 35 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 23 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 23 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 442 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 23 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 9 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 9 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 466 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 9 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 454 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 7 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 7 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 488 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 7 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 496 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 506 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 507 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 110 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 110 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 280 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 110 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 48 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 48 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 399 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 48 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 458 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |==                                                                    |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 50 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 50 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 369 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 50 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 27 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 27 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 422 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 27 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 11 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 11 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 11 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 27 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 27 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 410 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 27 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 449 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 482 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 437 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 477 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 491 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 493 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 188 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 188 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 177 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 188 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 107 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 107 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 302 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 107 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 57 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 57 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 383 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 57 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 102 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 102 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 310 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 102 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 60 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 60 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 383 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 60 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 26 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 26 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 436 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 26 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 480 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## Warning in variance_prior(ql_disp, df, covariate = gene_means, abundance_trend = ql_disp_trend): Variance prior estimate did not properly converge

## Warning in variance_prior(ql_disp, df, covariate = gene_means, abundance_trend = ql_disp_trend): Variance prior estimate did not properly converge

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 59 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 59 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 364 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 59 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 21 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 21 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 444 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 21 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 455 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 17 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 427 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 469 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 7 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 7 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 465 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 7 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 481 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 144 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 144 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 245 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 144 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 66 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 66 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 367 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 66 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                                                              |====                                                                  |   5%  |                                               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|====================================================================  |  98%  |                                                                              |===================================================================== |  99%  |                                                                              |======================================================================| 100%

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 38 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 38 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 411 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 38 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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|======================================================================| 100%

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 53 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 53 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 388 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 53 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 43 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 43 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 403 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 43 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |==                                                                    |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 18 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 18 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 439 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 18 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 34 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 34 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 400 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 34 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 440 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 458 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 439 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 14 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 454 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 6 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 459 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 5 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 468 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 122 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 122 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 298 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 122 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 53 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 53 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 455 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 53 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 23 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 23 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 514 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 23 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 56 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 56 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 442 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 56 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 33 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 33 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 497 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 33 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 10 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 10 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 552 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## Warning in variance_prior(ql_disp, df, covariate = gene_means, abundance_trend = ql_disp_trend): Variance prior estimate did not properly converge

## Warning in variance_prior(ql_disp, df, covariate = gene_means, abundance_trend = ql_disp_trend): Variance prior estimate did not properly converge

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 10 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero
## Warning: Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 26 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 26 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 503 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 26 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 555 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 11 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 11 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 561 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 11 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 523 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 8 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 3 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 3 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 565 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 3 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 4 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 4 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 574 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 4 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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|===================================================================== |  99%  |                                                                              |======================================================================|  99%  |                                                                              |======================================================================| 100%

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 584 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 112 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 112 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 253 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 112 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 61 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 61 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 340 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 61 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 32 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 32 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 390 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 32 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 463 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 1 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 464 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 56 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 56 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 359 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 56 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |==                                                                    |   4%  |                                               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|===================================================================== |  99%  |                                                                              |======================================================================| 100%

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 33 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 33 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 396 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 33 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 428 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 462 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 464 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 28 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 28 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 391 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 28 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 421 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 16 genes with only between-gene repressions.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 9 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 9 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 437 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 9 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 464 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                                                              |===                                                                   |   4%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 464 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 10 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 10 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 423 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 10 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 4 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 4 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 452 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 4 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 2 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 2 genes with only between-gene repressions.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 458 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Pruning 2 genes with only between-gene repressions.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

##   |                                                                              |                                                                      |   0%  |                                                                              |                                                                      |   1%  |                                                                              |=                                                                     |   1%  |                                                                              |=                                                                     |   2%  |                                                                              |==                                                                    |   2%  |                                                                              |==                                                                    |   3%  |                                               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|===================================================================== |  99%  |                                                                              |======================================================================|  99%  |                                                                              |======================================================================| 100%

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero
## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : Zero sample variances detected, have been offset away from zero

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 464 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## alpha_gt cannot be positive if there is no edge in the GRN, setting alpha for 464 links to zero.

## Prior versus data weight is tuned to be 100%.

## Converged.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.
## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## 
## Computing the association scores

## Computing regulons enrichment with aREA

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## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

## Warning in .AUCell_buildRankings(exprMat = exprMat, featureType = featureType,
## : nCores is no longer used. It will be deprecated in the next AUCell version.

## topTableF is obsolete and will be removed in a future version of limma. Please considering using topTable instead.

date <- Sys.Date()
date <- gsub(x=date, pattern="-", replacement="")
saveRDS(dfAUCAll, file=paste0("../objects/dfAUCAll_dyngen",date,"_discriminativePrior.rds"))

for(nn in 1:6){
  curdfAUC <- readRDS(paste0("../objects/dfAUCAll_dyngen",nn,".rds"))
  curdfAUC$nn <- nn

  if(nn==1){
    dfAUCAll <- curdfAUC
  } else {
    dfAUCAll <- rbind(dfAUCAll, curdfAUC)
  }
}

# dfAUCAll <- readRDS("../objects/dfAUCAll_dyngen20210502.rds")
dfAUCAll$method <- factor(dfAUCAll$method, 
                          levels = c("poisson", "poisson_lasso", "poisson_lasso_repr",
                                     "dirMult", "dirMult_lasso", "dirMult_lasso_repr",
                                     "dirMult_alphaEst", "dirMult_lasso_alphaEst", "dirMult_lasso_alphaEst_repr",
                                      "viper", "AUCell"))

ggplot(dfAUCAll, aes(x=method, y=auc)) +
  geom_boxplot(aes(col=method)) +
  facet_wrap(.~noiseTFs * noiseEdges, 
             ncol = length(nNoiseEdgeGrid), 
             nrow = length(nNoiseTFGrid)) +
  theme_bw() +
  theme(axis.text.x = element_blank(),
        axis.ticks.x = element_blank()) +
  scale_y_continuous(n.breaks=4) +
  xlab("") + ylab("AUC")

ggsave("../../plots/domino/aucAllSettings_dyngen_discriminativePrior.pdf", width=12, height=9)